git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
JAL-553 JAL-1557 always send selections after triggering the PaintRefreser for a...
[jalview.git]
/
src
/
jalview
/
ext
/
jmol
/
JalviewJmolBinding.java
diff --git
a/src/jalview/ext/jmol/JalviewJmolBinding.java
b/src/jalview/ext/jmol/JalviewJmolBinding.java
index
a1b6917
..
3f0847b
100644
(file)
--- a/
src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/
src/jalview/ext/jmol/JalviewJmolBinding.java
@@
-28,6
+28,7
@@
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.io.AppletFormatAdapter;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.io.AppletFormatAdapter;
+import jalview.io.StructureFile;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ResidueProperties;
import jalview.structure.AtomSpec;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ResidueProperties;
import jalview.structure.AtomSpec;
@@
-1121,7
+1122,7
@@
public abstract class JalviewJmolBinding extends AAStructureBindingModel
{
String fileName = modelfilenames[modelnum];
boolean foundEntry = false;
{
String fileName = modelfilenames[modelnum];
boolean foundEntry = false;
- MCview.PDBfile pdb = null;
+ StructureFile pdb = null;
String pdbfile = null;
// model was probably loaded inline - so check the pdb file hashcode
if (loadedInline)
String pdbfile = null;
// model was probably loaded inline - so check the pdb file hashcode
if (loadedInline)
@@
-1144,7
+1145,7
@@
public abstract class JalviewJmolBinding extends AAStructureBindingModel
{
pdb = getSsm().setMapping(getSequence()[pe], getChains()[pe],
pdbfile, AppletFormatAdapter.PASTE);
{
pdb = getSsm().setMapping(getSequence()[pe], getChains()[pe],
pdbfile, AppletFormatAdapter.PASTE);
- getPdbEntry(modelnum).setFile("INLINE" + pdb.id);
+ getPdbEntry(modelnum).setFile("INLINE" + pdb.getId());
matches = true;
foundEntry = true;
}
matches = true;
foundEntry = true;
}
@@
-1183,10
+1184,10
@@
public abstract class JalviewJmolBinding extends AAStructureBindingModel
if (matches)
{
// add an entry for every chain in the model
if (matches)
{
// add an entry for every chain in the model
- for (int i = 0; i < pdb.chains.size(); i++)
+ for (int i = 0; i < pdb.getChains().size(); i++)
{
{
- String chid = new String(pdb.id + ":"
- + pdb.chains.elementAt(i).id);
+ String chid = new String(pdb.getId() + ":"
+ + pdb.getChains().elementAt(i).id);
chainFile.put(chid, fileName);
chainNames.addElement(chid);
}
chainFile.put(chid, fileName);
chainNames.addElement(chid);
}